Mechanism and inhibition of the papain‐like protease, PLpro, of SARS‐CoV‐2
The SARS‐CoV‐2 coronavirus encodes an essential papain‐like protease domain as part of its non‐structural protein (nsp)‐3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin‐like ISG15 protein modifications as well as, with lower activity, Lys48‐linked polyubiquitin....
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| Vydáno v: | The EMBO journal Ročník 39; číslo 18; s. e106275 - n/a |
|---|---|
| Hlavní autoři: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
London
Nature Publishing Group UK
15.09.2020
Springer Nature B.V John Wiley and Sons Inc |
| Témata: | |
| ISSN: | 0261-4189, 1460-2075, 1460-2075 |
| On-line přístup: | Získat plný text |
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| Abstract | The SARS‐CoV‐2 coronavirus encodes an essential papain‐like protease domain as part of its non‐structural protein (nsp)‐3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin‐like ISG15 protein modifications as well as, with lower activity, Lys48‐linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin‐binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non‐covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self‐processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS‐CoV‐2 infection model.
Synopsis
Crystal structures explain the specificity of SARS‐CoV‐2 papain‐like protease, PLpro, for ISG15 and Lys48‐linked diubiquitin, and specific inhibition of PLpro by small molecules, shows strong antiviral effects.
SARS‐CoV-2 PLpro preferentially cleaves ISG15 and also targets longer Lys48‐linked ubiquitin chains.
Preference for ISG15 is provided by the S1 ubiquitin binding site in PLpro, while Lys48‐polyubiquitin specificity is provided by the S2 ubiquitin binding site.
In a high‐throughput screen, FDA approved drugs and late stage clinical compounds are unable to inhibit PLpro
in vitro
.
Known SARS PLpro inhibitors also target SARS2 PLpro and show anti‐viral efficacy.
Graphical Abstract
Crystal structure and biochemical analysis explains the specificity of SARS‐CoV‐2 PLpro for ISG15 and longer Lys48‐linked ubiquitin chains leading to the identification of inhibitors that show promising antiviral activity in a SARS‐CoV‐2 infection model. |
|---|---|
| AbstractList | The SARS‐CoV‐2 coronavirus encodes an essential papain‐like protease domain as part of its non‐structural protein (nsp)‐3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin‐like ISG15 protein modifications as well as, with lower activity, Lys48‐linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin‐binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non‐covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self‐processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS‐CoV‐2 infection model. The SARS‐CoV‐2 coronavirus encodes an essential papain‐like protease domain as part of its non‐structural protein (nsp)‐3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin‐like ISG15 protein modifications as well as, with lower activity, Lys48‐linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin‐binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non‐covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self‐processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS‐CoV‐2 infection model. Crystal structure and biochemical analysis explains the specificity of SARS‐CoV‐2 PLpro for ISG15 and longer Lys48‐linked ubiquitin chains leading to the identification of inhibitors that show promising antiviral activity in a SARS‐CoV‐2 infection model. The SARS‐CoV‐2 coronavirus encodes an essential papain‐like protease domain as part of its non‐structural protein (nsp)‐3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin‐like ISG15 protein modifications as well as, with lower activity, Lys48‐linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin‐binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non‐covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self‐processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS‐CoV‐2 infection model. Synopsis Crystal structures explain the specificity of SARS‐CoV‐2 papain‐like protease, PLpro, for ISG15 and Lys48‐linked diubiquitin, and specific inhibition of PLpro by small molecules, shows strong antiviral effects. SARS‐CoV-2 PLpro preferentially cleaves ISG15 and also targets longer Lys48‐linked ubiquitin chains. Preference for ISG15 is provided by the S1 ubiquitin binding site in PLpro, while Lys48‐polyubiquitin specificity is provided by the S2 ubiquitin binding site. In a high‐throughput screen, FDA approved drugs and late stage clinical compounds are unable to inhibit PLpro in vitro . Known SARS PLpro inhibitors also target SARS2 PLpro and show anti‐viral efficacy. Graphical Abstract Crystal structure and biochemical analysis explains the specificity of SARS‐CoV‐2 PLpro for ISG15 and longer Lys48‐linked ubiquitin chains leading to the identification of inhibitors that show promising antiviral activity in a SARS‐CoV‐2 infection model. The SARS-CoV-2 coronavirus encodes an essential papain-like protease domain as part of its non-structural protein (nsp)-3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin-like ISG15 protein modifications as well as, with lower activity, Lys48-linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin-binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non-covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self-processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS-CoV-2 infection model.The SARS-CoV-2 coronavirus encodes an essential papain-like protease domain as part of its non-structural protein (nsp)-3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin-like ISG15 protein modifications as well as, with lower activity, Lys48-linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin-binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non-covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self-processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS-CoV-2 infection model. The SARS‐CoV‐2 coronavirus encodes an essential papain‐like protease domain as part of its non‐structural protein (nsp)‐3, namely SARS2 PLpro, that cleaves the viral polyprotein, but also removes ubiquitin‐like ISG15 protein modifications as well as, with lower activity, Lys48‐linked polyubiquitin. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin‐binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. To identify PLpro inhibitors in a repurposing approach, screening of 3,727 unique approved drugs and clinical compounds against SARS2 PLpro identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non‐covalent small molecule SARS PLpro inhibitors also target SARS2 PLpro, prevent self‐processing of nsp3 in cells and display high potency and excellent antiviral activity in a SARS‐CoV‐2 infection model. Synopsis Crystal structures explain the specificity of SARS‐CoV‐2 papain‐like protease, PLpro, for ISG15 and Lys48‐linked diubiquitin, and specific inhibition of PLpro by small molecules, shows strong antiviral effects. SARS‐CoV-2 PLpro preferentially cleaves ISG15 and also targets longer Lys48‐linked ubiquitin chains. Preference for ISG15 is provided by the S1 ubiquitin binding site in PLpro, while Lys48‐polyubiquitin specificity is provided by the S2 ubiquitin binding site. In a high‐throughput screen, FDA approved drugs and late stage clinical compounds are unable to inhibit PLpro in vitro. Known SARS PLpro inhibitors also target SARS2 PLpro and show anti‐viral efficacy. Crystal structure and biochemical analysis explains the specificity of SARS‐CoV‐2 PLpro for ISG15 and longer Lys48‐linked ubiquitin chains leading to the identification of inhibitors that show promising antiviral activity in a SARS‐CoV‐2 infection model. |
| Author | Lowes, Kym N Doerflinger, Marcel Allison, Cody C Dewson, Grant Kuchel, Nathan W van der Heden van Noort, Gerbrand J Pellegrini, Marc Bernardini, Jonathan P Mitchell, Jeffrey P Ebert, Gregor Klemm, Theresa Lu, Bernadine GC Blackmore, Timothy R Lessene, Guillaume Feltham, Rebecca Calleja, Dale J Gan, Zhong Yan Ovaa, Huib Shibata, Yuri Komander, David Au, Amanda E Grohmann, Christoph Newman, Janet Geurink, Paul P Richardson, Lachlan W Lechtenberg, Bernhard C Cooney, James P Czabotar, Peter E Riboldi‐Tunnicliffe, Alan |
| AuthorAffiliation | 5 Australian Synchrotron ANSTO Clayton Vic. Australia 2 Department of Biochemistry and Molecular Biology Michael Smith Laboratories University of British Columbia Vancouver BC Canada 6 Pharmacology and Therapeutics Department University of Melbourne Melbourne Vic. Australia 3 Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Centre Leiden The Netherlands 1 The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology University of Melbourne Melbourne Vic. Australia 4 Commonwealth Scientific and Industrial Research Organisation (CSIRO) Biomedical Program Parkville Vic. Australia |
| AuthorAffiliation_xml | – name: 5 Australian Synchrotron ANSTO Clayton Vic. Australia – name: 4 Commonwealth Scientific and Industrial Research Organisation (CSIRO) Biomedical Program Parkville Vic. Australia – name: 3 Oncode Institute and Department of Cell and Chemical Biology Leiden University Medical Centre Leiden The Netherlands – name: 1 The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology University of Melbourne Melbourne Vic. Australia – name: 2 Department of Biochemistry and Molecular Biology Michael Smith Laboratories University of British Columbia Vancouver BC Canada – name: 6 Pharmacology and Therapeutics Department University of Melbourne Melbourne Vic. Australia |
| Author_xml | – sequence: 1 givenname: Theresa orcidid: 0000-0002-2847-3550 surname: Klemm fullname: Klemm, Theresa organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 2 givenname: Gregor surname: Ebert fullname: Ebert, Gregor organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 3 givenname: Dale J orcidid: 0000-0002-8306-0900 surname: Calleja fullname: Calleja, Dale J organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 4 givenname: Cody C surname: Allison fullname: Allison, Cody C organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 5 givenname: Lachlan W orcidid: 0000-0001-8877-1376 surname: Richardson fullname: Richardson, Lachlan W organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 6 givenname: Jonathan P orcidid: 0000-0002-5767-7624 surname: Bernardini fullname: Bernardini, Jonathan P organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Department of Biochemistry and Molecular Biology, Michael Smith Laboratories University of British Columbia – sequence: 7 givenname: Bernadine GC orcidid: 0000-0001-8044-9710 surname: Lu fullname: Lu, Bernadine GC organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 8 givenname: Nathan W surname: Kuchel fullname: Kuchel, Nathan W organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 9 givenname: Christoph surname: Grohmann fullname: Grohmann, Christoph organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 10 givenname: Yuri surname: Shibata fullname: Shibata, Yuri organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 11 givenname: Zhong Yan orcidid: 0000-0001-5755-7780 surname: Gan fullname: Gan, Zhong Yan organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 12 givenname: James P orcidid: 0000-0003-3680-4644 surname: Cooney fullname: Cooney, James P organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 13 givenname: Marcel orcidid: 0000-0001-9159-3021 surname: Doerflinger fullname: Doerflinger, Marcel organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 14 givenname: Amanda E orcidid: 0000-0003-3656-2673 surname: Au fullname: Au, Amanda E organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 15 givenname: Timothy R orcidid: 0000-0001-7079-676X surname: Blackmore fullname: Blackmore, Timothy R organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 16 givenname: Gerbrand J orcidid: 0000-0001-5955-6431 surname: van der Heden van Noort fullname: van der Heden van Noort, Gerbrand J organization: Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre – sequence: 17 givenname: Paul P surname: Geurink fullname: Geurink, Paul P organization: Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre – sequence: 18 givenname: Huib surname: Ovaa fullname: Ovaa, Huib organization: Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Centre – sequence: 19 givenname: Janet orcidid: 0000-0003-2666-3219 surname: Newman fullname: Newman, Janet organization: Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program – sequence: 20 givenname: Alan orcidid: 0000-0003-2244-2486 surname: Riboldi‐Tunnicliffe fullname: Riboldi‐Tunnicliffe, Alan organization: Australian Synchrotron, ANSTO – sequence: 21 givenname: Peter E surname: Czabotar fullname: Czabotar, Peter E organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 22 givenname: Jeffrey P surname: Mitchell fullname: Mitchell, Jeffrey P organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 23 givenname: Rebecca surname: Feltham fullname: Feltham, Rebecca organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 24 givenname: Bernhard C orcidid: 0000-0002-5674-6894 surname: Lechtenberg fullname: Lechtenberg, Bernhard C organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 25 givenname: Kym N surname: Lowes fullname: Lowes, Kym N organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 26 givenname: Grant orcidid: 0000-0003-4251-8898 surname: Dewson fullname: Dewson, Grant organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 27 givenname: Marc orcidid: 0000-0003-3627-3126 surname: Pellegrini fullname: Pellegrini, Marc email: pellegrini@wehi.edu.au organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne – sequence: 28 givenname: Guillaume orcidid: 0000-0002-1193-8147 surname: Lessene fullname: Lessene, Guillaume email: glessene@wehi.edu.au organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, Pharmacology and Therapeutics Department, University of Melbourne – sequence: 29 givenname: David orcidid: 0000-0002-8092-4320 surname: Komander fullname: Komander, David email: dk@wehi.edu.au organization: The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/32845033$$D View this record in MEDLINE/PubMed |
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| Snippet | The SARS‐CoV‐2 coronavirus encodes an essential papain‐like protease domain as part of its non‐structural protein (nsp)‐3, namely SARS2 PLpro, that cleaves the... The SARS-CoV-2 coronavirus encodes an essential papain-like protease domain as part of its non-structural protein (nsp)-3, namely SARS2 PLpro, that cleaves the... |
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| SubjectTerms | Animals Antiviral activity Antiviral agents Antiviral Agents - pharmacology Antiviral drugs Binding Sites Chains Chlorocebus aethiops Coronavirus 3C Proteases - antagonists & inhibitors Coronavirus 3C Proteases - chemistry Coronavirus 3C Proteases - genetics Coronavirus 3C Proteases - metabolism Coronaviruses COVID-19 Crystal structure Crystallography, X-Ray Cytokines - genetics Drug Evaluation, Preclinical - methods Drug Repositioning Drugs EMBO23 EMBO31 EMBO40 Fluorescence Polarization HEK293 Cells Humans Inhibitors ISG15 Kinases Kinetics Models, Molecular Papain papain‐like protease Protease Protease Inhibitors - pharmacology Protein Conformation Proteinase Proteins SARS-CoV-2 - chemistry SARS-CoV-2 - genetics SARS-CoV-2 - metabolism Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 small molecule inhibitor Ubiquitin Ubiquitin - metabolism Ubiquitins - genetics Vero Cells Viral diseases |
| Title | Mechanism and inhibition of the papain‐like protease, PLpro, of SARS‐CoV‐2 |
| URI | https://link.springer.com/article/10.15252/embj.2020106275 https://onlinelibrary.wiley.com/doi/abs/10.15252%2Fembj.2020106275 https://www.ncbi.nlm.nih.gov/pubmed/32845033 https://www.proquest.com/docview/2442518386 https://www.proquest.com/docview/2437397341 https://pubmed.ncbi.nlm.nih.gov/PMC7461020 |
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